R26 Using phylogenetic trees

Question 1

What type of trees show individuals are related to one another ?

Answer 1

Gene trees

Question 2

What are the key components to a gene tree ?

Answer 2

o Each leaf-node is a unique copy of a specific gene (usually mitochondrial locus cytochrome oxidase 1 (Cox1) sampled from a set of individuals
o Each internal node is an ancestor
o Gene trees often reflect population structure and history

Question 3

How has the mitochondrial DNA changed over time ?

Answer 3

• Mitochondrial are maternally inherited, no recombination, the most recent common ancestor (MRCA) is a female called mitochondrial eve. She had several daughters
  o Mt copies fixed due to chance (genetic drift)
  o There is no recombination of mitochondrial DNA

Question 4

How has the Y-chromosome changed over time ?

Answer 4

Y-Adam – Y chromosome does not recombine so it strictly paternally inherited
- Most recent common ancestor of all Y chromosome copies

Question 5

How does recombination effect phylogeny in diploid sexual organisms ?

Answer 5

Recombination leads to switches in ancestry in diploid sexual organisms
- Meaning we have a different set of ancestors at each position of the genome
- Most gene trees are the random outcome of genetic drift

Question 6

Did Y-Adam live at the same time as mt-Eve? How can we tell ?

Answer 6

• We expect the MRCA for the mt and Y to be the same time point
• Model simulation can tell us this once plotted on a histogram
• We expect both of them to exist 10,000 generations ago

Question 7

What is meant by monophyletic ?

Answer 7

A monophyletic group of species shares a single common ancestor and also includes all of the descendants of that common ancestor

Question 8

What was the effect of neanderthal introgression?

Answer 8

• Toll-like receptors, on the macrophages involved in innate immunity being added to the organisms leading to allergies

Question 9

How does the ancestry of recombining genomes work ?

Answer 9

Create a mosaic of gene trees
- Sexual organisms have 1 breakpoint per generation per chromosome
- Recombination events lead to switches in ancestry
- We have different set of ancestors at each position of the genome
- Most gene tree variation is the random outcome of genetic drift

Question 10

What is meant by topology ?

Answer 10

branching structure of the tree

Question 11

What is incomplete lineage sorting ?

Answer 11

• Gene trees from young species are paraphyletic (descended from a common ancestor but mot including all the descendant groups)
• Largely reflect random variation in the ancestral species

Question 12

Individual ancestry is captured by … trees, in sexual organism’s gene trees vary along the genome due to …

Answer 12

gene , recombination

Question 13

Bifurcating trees are ?

Answer 13

divide into two branches or fork

Question 14

How does hybridisation change the topology of the tree ?

Answer 14

 Nothing
 Merge (a new specie with half and half)
 Invasion of one specie (other species is diluted by the other in the offspring’s genome)
 Form hybrid zones (areas of the animal are one specie and other areas are another)
 Exchange few genes (introgression)
 Form new hybrid species

Question 15

What is adaptive introgression ?

Answer 15

When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool. Can be detected using gene tree topologies

Question 16

What is Allopolyploid speciation ?

Answer 16

very common in plants, hybridisation between two species
- Unreduced gametes  both genome copies are retained

Question 17

What is homoploid hybrid speciation ?

Answer 17

: hybridisation can lead to new species without genome duplication

Question 18

What will happen to the hybrid generation in homoploid hybrid speciation ?

Answer 18

• BDMIs will be selected out in subsequent hybrid generations
• Eventually only compatible combos of parental alleles remain
• Hybrid may be fitter than either parental species